Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/imp
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Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
BiocManager::install("rtracklayer")GRanges objects using import and export.browserSession.track<- function.ucscTableQuery and getTable.GenomicRanges instead.GenomicAlignments or Rsamtools instead, as rtracklayer is designed for annotation tracks.GRanges in R.import or export.browserSession.GRanges object specifying the genomic segment to view or download.ucscTableQuery.ucscTableQuery.GRangesForUCSCGenome to formally associate interval data with a UCSC genome build and validate bounds before uploading.GRanges tracks before uploading or viewing (e.g., targetTrack[1:10]) to avoid overwhelming the browser session.export and import which derives the format from the file extension.GRanges use 1-based coordinates, while formats like BED use 0-based. Fix: rtracklayer handles this automatically during import/export, so avoid manual coordinate shifting.browseGenome to load tracks and set the view in a single call.This skill is the knowledge layer — when, why, and how to use rtracklayer. To run this analysis on your own data with managed compute, automated QC, and reproducible outputs, use BioMate — free to start.
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概要と使いどころ
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
日本語の概要は準備中です。原文の説明を表示しています。
This tool uses the label-tree function from HyPhy to annotate a phylogenetic tree. It allows users to select a subset of leaves using either a regular expression or a list of sequence names, and then apply a specified label to these selecte
日本語の概要は準備中です。原文の説明を表示しています。
This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
日本語の概要は準備中です。原文の説明を表示しています。
apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
日本語の概要は準備中です。原文の説明を表示しています。
ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).
日本語の概要は準備中です。原文の説明を表示しています。
AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
日本語の概要は準備中です。原文の説明を表示しています。